Although it is possible to diagnose primary high-grade thyroid lymphoma from a fine needle aspiration (FNA) biopsy, the distinction of low-grade B-cell lymphoma of mucosa-associated lymphoid tissue (MALT) from lymphocytic thyroiditis is sometimes problematic. Definitive diagnosis of lymphoma on cytologic specimens may be facilitated by the documentation of a clonal lymphoid proliferation within the specimen by flow cytometric immunophenotyping or immunocytochemistry. Recently, molecular techniques have also been developed to detect clonal lymphoid proliferation based on immunoglobulin (Ig) or T-cell receptor gene rearrangement. We have used a polymerase chain reaction (PCR)-based assay for Ig heavy chain gene arrangement to identify a clonal population of lymphocytes within the thyroid FNA specimen from a low-grade thyroid MALT lymphoma. Using this assay, we identified no distinct clonal population in five cytologic specimens of lymphocytic thyroiditis. Therefore, this PCR-based clonality assay represents a potentially useful adjunct to the cytologic diagnosis of thyroid lymphoma.